TY - JOUR
T1 - Sequence-dependent model of genes with dual σ factor preference
AU - Baptista, Ines S.C.
AU - Kandavalli, Vinodh
AU - Chauhan, Vatsala
AU - Bahrudeen, Mohamed N.M.
AU - Almeida, Bilena L.B.
AU - Palma, Cristina S.D.
AU - Dash, Suchintak
AU - Ribeiro, Andre S.
N1 - Funding Information:
This work was supported by the Jane and Aatos Erkko Foundation [ 10-10524-38 to A.S.R]; Finnish Cultural Foundation [ 00200193 and 00212591 to I.S.C.B., and 50201300 to S.D.]; Pirkanmaa Regional Fund of the Finnish Cultural Foundation to V.K.; Suomalainen Tiedeakatemia to C.S.D.P.; Tampere University Graduate Program to V.C., M.N.M.B., and B.L.B.A.; EDUFI Fellowship [TM-19-11105 to S.D]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Publisher Copyright:
© 2022 The Authors
Preprint available https://doi.org/10.1101/2021.11.17.468920
PY - 2022/4
Y1 - 2022/4
N2 - Escherichia coli uses σ factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single σ factor, approximately 5% of them have dual σ factor preference. The most common are those responsive to both σ70, which controls housekeeping genes, and σ38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that ‘σ70+38 genes’ are nearly as upregulated in stationary growth as ‘σ38 genes’. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ38 levels. We then propose and validate a sequence dependent model of σ70+38 genes, with dual sensitivity to σ38 and σ70, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and σ factor combinations. Given this, promoters controlling σ70+38 genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.
AB - Escherichia coli uses σ factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single σ factor, approximately 5% of them have dual σ factor preference. The most common are those responsive to both σ70, which controls housekeeping genes, and σ38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that ‘σ70+38 genes’ are nearly as upregulated in stationary growth as ‘σ38 genes’. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ38 levels. We then propose and validate a sequence dependent model of σ70+38 genes, with dual sensitivity to σ38 and σ70, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and σ factor combinations. Given this, promoters controlling σ70+38 genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.
KW - Dual σ factor preference
KW - E. coli
KW - Flow cytometry
KW - RNA-seq
KW - Sequence-dependent gene expression model
U2 - 10.1016/j.bbagrm.2022.194812
DO - 10.1016/j.bbagrm.2022.194812
M3 - Article
C2 - 35338024
VL - 1865
JO - Biochimica et Biophysica Acta: Gene Regulatory Mechanisms
JF - Biochimica et Biophysica Acta: Gene Regulatory Mechanisms
SN - 1874-9399
IS - 3
M1 - 194812
ER -